Aims

The STRENDA project focuses on three main aims: The establishment of publication standards for enzyme activity data, the standardization of assay conditions and the development of STRENDA DB, an electronic validation and storage system for functional enzyme data.

1. Publication standards

The STRENDA Commission establishes standards of reporting enzyme data to ensure that the conditions under which they were obtained are comprehensively described. Through extensive interactions with the biochemistry community the Commission has drawn up the STRENDA Guidelines that consist of two lists: List Level 1A defines the data that are required for a complete description of the materials and methods which were used in the experiments. List Level 1B defines the parameters to describe the enzyme activity data.

A formal description as well as both lists can be found under Guidelines.

Today more than 30 international biochemistry journals recommend their authors to consult the STRENDA Guidelines when publishing enzyme kinetics data.

The STRENDA Guidelines are reviewed on a regular basis with regards to their practical applicability, and to ensure that they cover current techniques. STRENDA shares MIRAGEPSI and many other guideline initiatives (for more projects see biosharing.org) two fundamental criteria to be broadly accepted by the science community [1,2]:

  • sufficiency: "The … guidelines should require sufficient information about a data set and its experimental context to allow a reader to understand and critically evaluate the interpretation and conclusions, and to support their experimental corroboration."
  • practicability: "Achieving compliance ... should not be so burdensome as to prohibit its widespread use."

References

[1] Taylor CF et al. (2007) The minimum information about a proteomics experiment (MIAPE). Nat Biotechnol. 25(8):887-893. doi:10.1038/nbt1329

[2] York WS et al. (2014) MIRAGE: The minimum information required for a glycomics experiment. Glycobiology 24(5):402–406. doi:10.1093/glycob/cwu018.

2. Standardization of Assay Conditions

A second goal of the STRENDA Commission is to derive uniform assay standards for the standardization of data for single enzymes and groups of enzymes. The conditions under which an enzyme operates depend on the organism and organelle in which it occurs. For example, the physiological temperature at which an enzyme operates in a mammal may have little relevance to the behaviour of the corresponding enzyme in a hyperthermophile. On the other hand, using very different assay conditions for assaying the forward and reverse reactions catalyzed by the same enzyme may mean that valuable thermodynamic data are lost.

The basis of initial assay standards can be the physiological conditions, which are those conditions in which cells, tissues, organs, or even the whole organism are present. However, these conditions first need to be determined.

First attempts towards the standardization of the assay conditions were made when compiling List Level 2. This list is still in a rudimentary state and currently subject of intense discussions within the Commission.

In collaboration with a number of various Dutch working groups, a standard assay for the enzymes from the glycolysis of baker's yeast has been defined and tested resulting in obtaining the essential kinetics of all enzymes involved in this pathway. This approach can be regarded as proof-of-principle which can be applied with modifications for the characterization of additional metabolic pathways (van Eunen et al. (2010) FEBS J. 277(3):749-760).

3. StRENDA DB - an Electronic validation and storage system
for functional enzyme data

STRENDA DB is an electronic validation  and storage system for functional enzyme data that aims at being integrated into the publication practices of the community and into the publication processes of the journals.

It incorporates the STRENDA Guidelines and provides the science community with a validation service that checks manuscript data on compliance with the Guidelines prior or during the publication process.

Users receive warnings informing them when necessary information is missing. A successful formal compliance is confirmed by the awarding of a STRENDA Registry Number (SRN) and documented in a fact sheet (PDF) containing all input data that can be submitted with the manuscript to the journal.

In addition, each dataset is assigned a DOI that allows reference and tracking of the data. The data become publicly available in the database only after the corresponding article has been peer-reviewed and published in a journal.

STRENDA DB is now operational in version 1.0 (www.strenda-db.org). The system is carefully maintained and subjected to continuous technical advancement. The Commission welcomes contact from the community for requests for further information, reporting any potential errors, as well as  suggestions for improvements  at strenda@beilstein-institut.de.